Defines many S4 generic functions used in Bioconductor
Home Page: https://bioconductor.org/packages/BiocGenerics
BiocGenerics is an R/Bioconductor package that defines many S4 generic functions used in Bioconductor.
See https://bioconductor.org/packages/BiocGenerics for more information including how to install the release version of the package (please refrain from installing directly from GitHub).
Consider the following:
library(BiocGenerics)
which # says it's defined in BiocGenerics
library(Matrix)
which # says it's defined in baseThis has the following consequences:
library(GenomicRanges)
example(GRanges, echo=FALSE)
which(seqnames(gr) %in% "chr2") # all is well
library(Matrix)
which(seqnames(gr) %in% "chr2")
## Error in which(seqnames(gr) %in% "chr2") :
## argument to 'which' is not logicalNot sure what the best solution is but at worst we could just use the Matrix version of the generic.
R Under development (unstable) (2020-02-18 r77829)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /Users/luna/Software/R/trunk/lib/libRblas.dylib
LAPACK: /Users/luna/Software/R/trunk/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Matrix_1.2-18 GenomicRanges_1.39.2 GenomeInfoDb_1.23.13
[4] IRanges_2.21.3 S4Vectors_0.25.12 BiocGenerics_0.33.0
loaded via a namespace (and not attached):
[1] zlibbioc_1.33.1 compiler_4.0.0 tools_4.0.0
[4] XVector_0.27.0 GenomeInfoDbData_1.2.2 RCurl_1.98-1.1
[7] grid_4.0.0 bitops_1.0-6 lattice_0.20-40
Hi, since this commit (69e6fad) it seems that the R-devel travis ci gives an warning if one uses the base which function and importing BiocGenerics.
See here for more information on it.
https://support.bioconductor.org/p/131811/
The warning is as follows:
Warning: multiple methods tables found for 'which'
Thank you in anticipation for sorting this out.
Best regards
Kristian Ullrich
It was added eight years ago, but I'm curious what's the reason for making S4 generics out of the parallel functions https://github.com/Bioconductor/BiocGenerics/blob/master/R/clusterApply.R resulting in:
> library(BiocGenerics)
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLBIs that really needed? Doesn't that just add unnecessary noise?
I have spent ~2 hours today trimming down a large code base to essentially this failing example code:
for (i in seq(2)) {
message(basename(glue::glue("/some/file")))
# ...
suppressPackageStartupMessages(library(BiocGenerics))
# ...
}which fails in the second iteration:
file
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘path’ for signature ‘"glue"’
Calls: fun ... message -> basename -> basename -> path -> <Anonymous>
Execution halted
Life would have been much easier if BiocGenerics functions masking base functions supported at least the same set of inputs:
glue_file <- glue::glue("/some/file")
base::basename(glue_file) # works
BiocGenerics::basename(glue_file) # failsI am building a package for bioconductor that works with singleCellExperiment objects and I have come across an issue with the conversion from DataFrame to data.frame. Specifically, because column names of a matrix can be duplicated, the row names of colData(sce) which are stored as a DataFrame can also be duplicated. The conversion to data.frame via the as.data.frame method always produces valid rownames via make.unique.
My issue (really an enhancement request) is that I would like this particular situation to throw an error by supplying the make.names = FALSE to as.data.frame, unfortunately all ... are ignored by the current version of the method. As I'm aware that handling some but not all ... arguments would cause confusion, I would like to request that make.names be exposed which would match the base S3 method for class 'matrix'.
Hi Hervé,
I am confused about an error on my topdownr package caused by as.data.frame generic:
Warning in as.data.frame.numeric(value, row.names = row.names, optional = optional, :
Direct call of 'as.data.frame.numeric()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
Error in value[3L] :
converted from warning: Direct call of 'as.data.frame.numeric()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
The backtrace of one of my unit tests is:
── Warning (test_utils.R:158:5): .groupByLabels ────────────────────────────────
Direct call of 'as.data.frame.integer()' is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test_utils.R:158:5
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─topdownr:::.groupByLabels(DF, c("ID", "LE"))
5. ├─BiocGenerics::as.data.frame(x) at topdownr/R/utils.R:241:5
6. └─S4Vectors::as.data.frame(x)
7. └─S4Vectors (local) .local(x, row.names, optional, ...)
8. ├─BiocGenerics::lapply(...)
9. └─base::lapply(...)
10. └─S4Vectors (local) FUN(X[[i]], ...)
11. ├─BiocGenerics::as.data.frame(col, optional = optional)
12. ├─base::as.data.frame(col, optional = optional)
13. └─base::as.data.frame.integer(col, optional = optional)
14. └─base::.Deprecated(...)Do you have a
A MWE:
x <- 1L:3L
as.data.frame(x)
#> x
#> 1 1
#> 2 2
#> 3 3
library("BiocGenerics")
#>
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#>
#> IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#>
#> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
#> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
#> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
#> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#> Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
#> tapply, union, unique, unsplit, which.max, which.min
as.data.frame(x)
#> Warning in as.data.frame.integer(x): Direct call of 'as.data.frame.integer()'
#> is deprecated. Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> x
#> 1 1
#> 2 2
#> 3 3Created on 2024-03-15 with reprex v2.1.0
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R Under development (unstable) (2024-03-15 r86132)
#> os Debian GNU/Linux 12 (bookworm)
#> system x86_64, linux-gnu
#> ui X11
#> language en
#> collate de_DE.UTF-8
#> ctype de_DE.UTF-8
#> tz Europe/Berlin
#> date 2024-03-15
#> pandoc 2.19.2 @ /home/sebastian/.guix-profile/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> BiocGenerics * 0.49.1 2023-11-01 [1] Bioconductor
#> cli 3.6.2 2023-12-11 [1] CRAN (R 4.4.0)
#> digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.0)
#> evaluate 0.23 2023-11-01 [1] CRAN (R 4.4.0)
#> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.4.0)
#> fs 1.6.3 2023-07-20 [1] CRAN (R 4.4.0)
#> glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0)
#> htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.4.0)
#> knitr 1.45 2023-10-30 [1] CRAN (R 4.4.0)
#> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
#> reprex 2.1.0 2024-01-11 [1] CRAN (R 4.4.0)
#> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.4.0)
#> rmarkdown 2.26 2024-03-05 [1] CRAN (R 4.4.0)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0)
#> withr 3.0.0 2024-01-16 [1] CRAN (R 4.4.0)
#> xfun 0.42 2024-02-08 [1] CRAN (R 4.4.0)
#> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.4.0)
#>
#> [1] /home/sebastian/opt/R/lib/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────I looked at the as.data.frame generic which is just setGeneric("as.data.frame", signature="x"). Any idea to fix this?
Best wishes,
Sebastian
I was wondering why scater and SingleCellExperiment had rev-suggests from BiocGenerics, but scater::normalize is now defunct so these are no longer relevant.
IMO this generic is far too... generic for a relatively complex analytical step, but what's done is done.
I have started to receive the following error with my automatic deployment script to shinyapps:
I am using R version 4.2.1, which has remained consistent for my previous deployments. Based on the Bioconductor version being used (3.16), it should be able to download the correct version using Github Actions.
Hello,
I noticed an issue arises when trying to subset a GRanges object after BiocGenerics is attached (in this case by regioneR::getGenome).
The following produces an error when running it from within a one of my package's functions (but, oddly, not when I run it line-by-line):
if(!require("regioneR")) BiocManager::install("regioneR")
func <- function(chroms = c("chr6", "chr8")){
all_chrom <- regioneR::getGenome(genome ="hg19")
select_chrom <- all_chrom[GenomicRanges::seqnames(all_chrom) %in% chroms, ]
return(select_chrom)
}
func()error in evaluating the argument 'i' in selecting a method for function '[': 'match' requires vector arguments
Here is the full console output when running from within my R package.
You can see that the error occurs right after BiocGenerics gets attached.
Querying 1 samples.
Query: GSM4703766
Using build: hg19
Determining available file types.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
1 supplementary file(s) found:
- GSM4703766_GAWSU510-A549-H3K4me3-ChIP-rep2_AGTCAA_GAWSU510_CKDL200157349-1a-13_HC3LFBBXX_L2_PE_R1-2.fastq.sam_noDup_RPBM.bedgraph.gz
Computing peaks from bedGraph file.
Importing chromosomes: chr6
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname,
do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames,
sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max,
which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
expand.grid, I, unname
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
The masked version of 'hg19' is not installed. Using the unmasked version. This means that no automatic masking will be available.
+ Selecting available chromosomes.
error in evaluating the argument 'i' in selecting a method for function '[': 'match' requires vector argumentsSaving results ==> /var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T//RtmpdxqwBu/file832c2b34218grl.hg38.rds
I think this might have something to do with different behaviours between S4Vectors::%in% and BiocGenerics::%in%
Using grepl instead of %in% seems to work ok, both within and outside of my package function.
select_chrom <- all_chrom[grepl(paste(paste0("^",chroms,"$"),collapse = "|"),
as.character(GenomicRanges::seqnames(all_chrom))), ]Best,
Brian
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] regioneR_1.26.1 BSgenome.Hsapiens.UCSC.hg19_1.4.3
[3] BSgenome_1.62.0 rtracklayer_1.54.0
[5] Biostrings_2.62.0 XVector_0.34.0
[7] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1
[9] IRanges_2.28.0 S4Vectors_0.32.4
[11] BiocGenerics_0.40.0
loaded via a namespace (and not attached):
[1] utf8_1.2.2 reticulate_1.24-9000
[3] R.utils_2.11.0 tidyselect_1.1.2
[5] RSQLite_2.2.11 AnnotationDbi_1.56.2
[7] htmlwidgets_1.5.4 grid_4.1.0
[9] BiocParallel_1.28.3 XGR_1.1.8
[11] munsell_0.5.0 DT_0.22
[13] colorspace_2.0-3 OrganismDbi_1.36.0
[15] Biobase_2.54.0 filelock_1.0.2
[17] MACSr_1.2.0 knitr_1.38
[19] supraHex_1.32.0 rstudioapi_0.13
[21] DescTools_0.99.44 MatrixGenerics_1.6.0
[23] GenomeInfoDbData_1.2.7 bit64_4.0.5
[25] echoconda_0.99.5 rprojroot_2.0.2
[27] basilisk_1.6.0 vctrs_0.4.0
[29] generics_0.1.2 xfun_0.30
[31] biovizBase_1.42.0 BiocFileCache_2.2.1
[33] R6_2.5.1 AnnotationFilter_1.18.0
[35] bitops_1.0-7 cachem_1.0.6
[37] reshape_0.8.8 DelayedArray_0.20.0
[39] assertthat_0.2.1 promises_1.2.0.1
[41] BiocIO_1.4.0 scales_1.1.1
[43] nnet_7.3-17 rootSolve_1.8.2.3
[45] gtable_0.3.0 lmom_2.8
[47] ggbio_1.42.0 ensembldb_2.18.4
[49] rlang_1.0.2 clisymbols_1.2.0
[51] MungeSumstats_1.3.16 echodata_0.99.7
[53] splines_4.1.0 lazyeval_0.2.2
[55] GEOquery_2.62.2 gargle_1.2.0
[57] dichromat_2.0-0 hexbin_1.28.2
[59] checkmate_2.0.0 BiocManager_1.30.16
[61] yaml_2.3.5 reshape2_1.4.4
[63] GenomicFeatures_1.46.5 ggnetwork_0.5.10
[65] backports_1.4.1 httpuv_1.6.5
[67] Hmisc_4.6-0 RBGL_1.70.0
[69] tools_4.1.0 ggplot2_3.3.5
[71] ellipsis_0.3.2 RColorBrewer_1.1-2
[73] proxy_0.4-26 Rcpp_1.0.8.3
[75] plyr_1.8.7 base64enc_0.1-3
[77] progress_1.2.2 zlibbioc_1.40.0
[79] purrr_0.3.4 RCurl_1.98-1.6
[81] basilisk.utils_1.6.0 prettyunits_1.1.1
[83] rpart_4.1.16 SummarizedExperiment_1.24.0
[85] ggrepel_0.9.1 cluster_2.1.3
[87] here_1.0.1 fs_1.5.2
[89] crul_1.2.0 magrittr_2.0.3
[91] data.table_1.14.2 echotabix_0.99.5
[93] dnet_1.1.7 openxlsx_4.2.5
[95] gh_1.3.0 mvtnorm_1.1-3
[97] ProtGenerics_1.26.0 matrixStats_0.61.0
[99] xtable_1.8-4 mime_0.12
[101] patchwork_1.1.1 hms_1.1.1
[103] XML_3.99-0.9 jpeg_0.1-9
[105] gridExtra_2.3 testthat_3.1.3
[107] compiler_4.1.0 biomaRt_2.50.3
[109] tibble_3.1.6 crayon_1.5.1
[111] R.oo_1.24.0 htmltools_0.5.2
[113] later_1.3.0 echoannot_0.99.4
[115] tzdb_0.3.0 Formula_1.2-4
[117] tidyr_1.2.0 expm_0.999-6
[119] Exact_3.1 lubridate_1.8.0
[121] DBI_1.1.2 ExperimentHub_2.2.1
[123] dbplyr_2.1.1 MASS_7.3-56
[125] rappdirs_0.3.3 boot_1.3-28
[127] Matrix_1.4-1 readr_2.1.2
[129] brio_1.1.3 piggyback_0.1.1
[131] cli_3.2.0 R.methodsS3_1.8.1
[133] parallel_4.1.0 igraph_1.2.11
[135] pkgconfig_2.0.3 dir.expiry_1.2.0
[137] GenomicAlignments_1.30.0 RCircos_1.2.2
[139] foreign_0.8-82 osfr_0.2.8
[141] xml2_1.3.3 stringr_1.4.0
[143] VariantAnnotation_1.40.0 digest_0.6.29
[145] graph_1.72.0 httpcode_0.3.0
[147] htmlTable_2.4.0 gld_2.6.4
[149] restfulr_0.0.13 curl_4.3.2
[151] shiny_1.7.1 Rsamtools_2.10.0
[153] rjson_0.2.21 lifecycle_1.0.1
[155] nlme_3.1-157 jsonlite_1.8.0
[157] limma_3.50.1 fansi_1.0.3
[159] pillar_1.7.0 lattice_0.20-45
[161] GGally_2.1.2 KEGGREST_1.34.0
[163] fastmap_1.1.0 httr_1.4.2
[165] survival_3.3-1 googleAuthR_2.0.0
[167] waldo_0.4.0 interactiveDisplayBase_1.32.0
[169] glue_1.6.2 zip_2.2.0
[171] png_0.1-7 BiocVersion_3.14.0
[173] bit_4.0.4 Rgraphviz_2.38.0
[175] class_7.3-20 stringi_1.7.6
[177] blob_1.2.2 AnnotationHub_3.2.2
[179] latticeExtra_0.6-29 memoise_2.0.1
[181] dplyr_1.0.8 e1071_1.7-9
[183] ape_5.6-2
Just noticed 0527f88. Is the long-term recommendation to switch to importing these generics from Matrix rather than BiocGenerics? It wouldn't make a difference to me as a developer, but I could imagine that you might want to get rid of the redundant definitions in BiocGenerics at some point.
Hi @hpages, the latest changes of BiocGenerics seems to cause a common error across many packages in the dev build server (see https://bioconductor.org/checkResults/3.16/bioc-LATEST/crisprDesign/nebbiolo2-buildsrc.html for instance)
Error: processing vignette 'intro.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.matrix': dims [product 42] do not match the length of object [7]
--- failed re-building ‘intro.Rmd’
That error arises from BiocGenerics::unlist used in the crisprDesign package. Here's a simple reproducible example:
library(BiocGenerics)
library(S4Vectors)
df <- DataFrame(a=1:2, b=1:2)
df <- split(df, f=df$b)
BiocGenerics::unlist(df)with output
> unlist(df)
DataFrame with 2 rows and 2 columns
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'as.matrix': dims [product 4] do not match the length of object [2]
My sessionInfo:
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] S4Vectors_0.35.3 BiocGenerics_0.43.2
loaded via a namespace (and not attached):
[1] compiler_4.2.1 IRanges_2.31.2
Hello, I have installed the BioGenerics of newest version 0.32 on my linux server. But when I import it, I get the following error,
library(BiocGenerics)
Error in value[3L] :
Package ‘BiocGenerics’ version 0.30.0 cannot be unloaded:
Error in unloadNamespace(package) : namespace ‘BiocGenerics’ is imported by ‘GenomicRanges’, ‘XVector’, ‘S4Vectors’, ‘GenomeInfoDb’, ‘IRanges’ so cannot be unloaded
How to fix this problem? Thanks.
Hi,
I see that BiocGenerics:::replaceSlots is used and recommended in some places, e.g. https://www.bioconductor.org/packages/devel/bioc/vignettes/SummarizedExperiment/inst/doc/Extensions.html#37_Enabling_subsetting_operations
Now as we unfortunately know R CMD check does not really like using the ::: trick to get unexported functions from packages. And I also don't really like copying the code into our package just to circumvent this (plus possible license issues).
How about just exporting replaceSlots?
Thanks for considering.
Cheers
Daniel
i had a line of code calculating the variance of several numeric values failing unexpectedly. took me a long time to discover that BiocGenerics overwrites stats::var() when imported, and the errors i'm seeing is not from base var().
$ R
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> library(BiocGenerics)
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
> var(c(1,2,3))
Error in var(c(1, 2, 3)) : is.atomic(y) is not TRUE
> is.atomic(c(1,2,3))
[1] TRUE
> stats::var(c(1,2,3))
[1] 1
> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux trixie/sid
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blis-openmp/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: Australia/Sydney
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] compiler_4.4.1googling the "is.atomic" error message didn't lead to anything constructive--suggesting a more recent bug?
am i using the var() function correctly? (i mean, i wasn't expecting something that worked in stats::var() to NOT work in BiocGenerics::var() in the first place...)
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